2015 Pre-TDWG Training Workshop

Transcription

1 2015 Pre-TDWG Training Workshop September 2015 Multi-Media University Nairobi, Kenya (unless indicated otherwise below) The JRS Biodiversity Foundation awarded a grant to Tulane University to support African participants in the 2015 Biodiversity Information Standards (TDWG) conference in Nairobi, Kenya from 28 September to 1 October 2015, and a pre-tdwg biodiversity informatics training workshop. The aim of the pre-conference training activity is to increase the capacity of African biodiversity specialists to mobilize biodiversity data from their countries and to engage with TDWG. The aim of involving them in the TDWG conference is to catalyze collaborations among African participants and TDWG members that will help to sustain African engagement with TDWG for many years to come. The following are agendas for all of the types of training that will be offered. We ask participants in the workshop to indicate to us which training you are most interested in receiving. Please Hank Bart (hbartjr@tulane.edu).

2 PaleoCore Workshop - Nairobi, Kenya September 2015 Presenter: Denne N. Reed, University of Texas at Austin (reedd@austin.utexas.edu) Day 1 - Data Management Concepts and Fundamentals I. PaleoCore Overview 1. The goals of digital data management in paleoanthropology 2. PaleoCore s key aims and objectives a. Data standards b. Data collections tools c. Data repository 3. Aims and objectives for the workshop II. Introduction to spatial data management 1. What is spatial data? 2. Overview of databases and spatial databases 3. Open source software and spatial data management systems 4. Data standards for paleoanthropology III. PaleoCore basic ontology and terms 1. PaleoCore foundation ontology 2. PaleoCore implementation of Darwin Core terms 3. Comparison with other data standards: Dublin Core, ABCD IV. PaleoCore user accounts 1. Creating user accounts 2. Setting permissions 3. Using PaleoCore online and offline V. PaleoCore project initialization 1. PaleoCore target audience, key features and limitations 2. PaleoCore project initialization process 3. Scheduling PaleoCore project initialization VI. Mapping project schemas 1. Project schema documentation 2. Entering terms and linking to existing terms VII. Downloading Data from PaleoCore 1. Project permissions and access rights 2. Downloading publicly available data

3 3. Data download and exchange formats VIII. PaleoCore and QGIS 1. Introduction to GIS and open-source GIS 2. Connecting to PaleoCore data repositories from QGIS 3. GIS data and exchange formats IX. Discussion 1. PaleoCore and its place in the digital data management landscape 2. Digital data and access rights 3. Digitizing existing collections vs. incoming collections Day 2 - Field Data Collection using Mobile Devices I. Introduction to Mobile Data Collection Hardware (ios) 1. Overview of different mobile computing platforms: ios, Android, Windows 2. The menagerie of mobile devices: smart phones, tablets, Total Stations 3. Overview of Global Navigation Satellite Systems (GNSS) forms) II. Configuring GISPro and related apps 1. Creating projects in GIS Pro 2. Configuring settings 3. Installing and customizing the PaleoCore feature class (data collection III. Developing and fine tuning a data collection workflow 1. Overview of data collection methodologies 2. Data collection dos, don ts and gotchas 3. Developing data collection workflows 4. Backup...backup and backup again IV. Caching map tiles for use in the field 1. Overview of publicly available satellite imagery and map tiles 2. Acquiring digital imagery and maps 3. Caching tiles on mobile devices for use in the field V. Exporting data from GIS Pro and related apps 1. Exporting data through itunes 2. Export and exchange formats 3. Creating backups VI. Uploading data to PaleoCore 1. Importing data to PaleoCore 2. Editing data online

4 2-Day Data Carpentry Workshop Nairobi Kenya, September 2015 Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. Our curriculum includes: Day 1 morning: Data organization in spreadsheets and data cleaning with OpenRefine Day 1 afternoon: Intro to and Data management in SQL Day 2 morning: Introduction to R or Python based on attendees preference Day 2 afternoon: We will select a topic based on our attendees preference The concepts, skills, and tools we teach are domain-independent, but example problem cases and datasets will be taken from organismal and evolutionary biology, biodiversity science, ecology, and environmental science. Data Carpentry's teaching is hands-on, so participants are required to bring their own laptops. (We will provide instructions on setting up the required software several days in advance) There are no pre-requisites, and we will assume no prior knowledge about the tools. Data Carpentry Agenda Day 1 8:30 Welcome and Introduction 9:00 Data organization in spreadsheets (hands-on) 10:15 tea / coffee break 10:45 Using Open Refine to clean data (hands-on) 12:00 lunch 1:00 Intro to Databases and Getting started with SQL 2:30 tea / coffee break 3:00 Manipulating data in SQL 4:00 Review and Wrap up Data Carpentry Agenda Day 2 8:30 Introducing Day 2 (Framework) 8:45 Intro to R and R Studio, Starting with data, Data frames (or Intro to Python and ipython Notebook) 10:15 tea / coffee break 10:45 Manipulating data in R (or Python) 12:00 lunch 1:00 Choose: cleaning data with R using web APIs best practices for organizing your project to facilitate Reproducible Research intro to relevant data standards for biodiversity data 2:30 tea / coffee break 3:00 continue from 1 pm choice 4:00 Review and Wrap up Funding: idigbio is funded by a grant from the National Science Foundation's Advancing Digitization of Biodiversity Collections Program (Cooperative Agreement EF ). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Data Carpentry has been supported by a contribution from the Moore Foundation and by the Gordon and Betty Moore Foundation s Data-Driven Discovery Initiative through grant GBMF4563 to Ethan White.

5 Instructors. o Matthew Collins, Senior Systems Programmer at idigbio. Matt assisted at the first Data Carpentry workshop and has since also instructed at three Data Carpentry and Software Carpentry workshops as well as idigbio-specific workshops and with the UF Data Science and Informatics student organization. He has taught Intro to SQL, Intro to Python, Intro to Shell, and Intro to web APIs with R. o Deborah Paul, Technology Specialist at idigbio. Deb has assisted at two Data Carpentry workshops, wrote and presented the Open Refine material, and has taught biodiversity data standards and best practices for digitization at several idigbio workshops. Deb has also facilitated many idigbio workshops and collaboratively put together the current idigbio Biodiversity Informatics Skills workshop series. She has experience with SQL in addition to covering the better-spreadsheet and Open Refine lessons. Assistants. o Libby Ellwood, idigbio post-doc. Libby has been to a Data Carpentry workshop and has experience with R and is an experienced teacher. She is a researcher studying phenology and is a key member of the team at idigbio working on ways to engage citizen scientists in collections digitization. o Kevin Love, idigbio Technology Specialist, has assisted at many Data Carpentry and idigbio workshops and also provides support for web conferencing and recording during workshops. Before the Workshop Setup and Software Installation To participate in this Data Carpentry workshop, you will need working copies of the software described at the setup page. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Instructors and helpers will be available starting at 8:30am both days to help with any installation issues. Please bring your own laptop and power cord, and plan to come early if you do not have all the required software installed. Setup Instructions [we will add this link soon] Workshop surveys It's important for the instructors to know who the audience is for each workshop. To give us information about the participants for the workshop, please fill out a brief pre-workshop survey before the workshop. Pre-workshop survey [we will add this link soon] You will also receive a post-workshop survey after the workshop so you can provide feedback and help us gauge the effectiveness of the materials. Note: The BIS-TDWG 2015 Conference includes a workshop session on the background of the Data Carpentry model and how any group can start using this model for workforce training. Questions? Please contact either Deb Paul (dpaul@fsu.edu) or Matt Collins (mcollins@acis.ufl.edu) for more information. Funding: idigbio is funded by a grant from the National Science Foundation's Advancing Digitization of Biodiversity Collections Program (Cooperative Agreement EF ). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Data Carpentry has been supported by a contribution from the Moore Foundation and by the Gordon and Betty Moore Foundation s Data-Driven Discovery Initiative through grant GBMF4563 to Ethan White.

6 SPECIFY 6 Session 1: Installation/Implementation/Setup Pre-installation decision-making process Conversion: Existing Specify 5 users New users conversion, wizard, WorkBench Data cleanup, parsing etc. Full Specify vs. Specify EZDB Mobile Specify stand alone WorkBench Installation TRAINING AGENDA MySQL 5.6 o GUI Tool interface database and user management Java 7 Specify o Specify o Specify1G o SpWizard o SpBackupRestore o SpiReports o ImportFileSplitter o DataExporter o SchemaExporter Data model and hierarchy information Institution, Discipline, Division, Collection, User Group, User Wizard database creation MySQL root username/password and database name Master U/P Security CM username and password Institutional information Accessions Accession Number setup (global only) Field formatting editor Storage tree definition setup

7 Division information Discipline type and name Taxon tree definition setup Pre-loading of taxon tree data Geography tree definition setup Collection information Catalog number setup Accession Number setup (collection level) Summary and build Post-installation decision-making process Setting up additional disciplines, collections Trees and tree definitions Form customization Reports Data conversion Consortia Session 2: Program interface, layout and navigation Specify login Username and password (from Wizard or provided) Database name (from Wizard) Port Generate key process Interface, layout and navigation Main menu Task bar Simple search Side bar Main pane Tabs Drag and drop Record sets

8 SPECIFY 6 Session 3: Data entry and editing Entering data Tables and sidebar configuration Field types o Text o Number o Formatted number o Date o Formatted/partial date o System pick list o User customizable pick list user defined, field, table o Query Combo Box o Required fields Sub form types Carry forward Save and New Auto numbering Locality features o Lat Long preference pane o GeoLocate o Google Earth o WorldWind o Clone tool Series data entry - limit 500 records Editing data TRAINING AGENDA Edit and View modes Batch identify Session 4: Working with Trees Taxonomy o Expanding o Find o Navigating tree o Split screen o Add node o Edit

9 o Move o Synonym o Associated Collection Objects and numbering o Merge Geography Storage Paleo Tree definitions Locking and unlocking trees Session 5: Querying data Searching for data using the Query builder Tables and Sidebar configuration Adding fields Adding aggregated or formatted tables Operators, Criteria, Sort, Show, Prompt Changing order of fields Removing fields Search Synonyms, Distinct, Count Wildcards (*) Higher level tree rank searches Result bar options 20,000 row limit o Record set, form view, print grid, export, Reports Searching for data using the Simple search All vs. Distinct table Primary vs. related searches Wildcards (*,, ) Configuration Result bar options o Record set, form view, print grid, export, Reports Global search coming in future release

10 SPECIFY 6 TRAINING AGENDA Session 6: WorkBench Import data 4000 row limit Import file splitter Data mapping Find Ctl-F Add, remove rows Edit cells Map satellite and Google Earth GEOLocate Convert Geocoordinate formats Export data set Images Carry forward Form view and customization Validation Create record set from data set coming in future release Uploading o Validate o Upload o Undo o Data integrity (future release) Reports Session 7: Interactions (Loans/Gifts/Borrows etc.) Tables and sidebar configuration Accession and repository agreement Loan o Adding preparations manual vs. record set o Returning loans Gift Borrow Exchange in and out Information request

11 Session 8: Attachments and images Viewing attachments Attachment browser Query Attaching attachments Import attachments Import attachments mapping file Drag and drop Session 9: Preferences and Security Editing Preferences Main menu Formatting System Trees Taskbar Google Earth MySQL Login Dialog Working with Security Security levels Manager, Full access, Limited Access, Guest Multiple disciplines Creating new users new and existing Group permissions Tables View, Add, Modify, Delete Tools Preferences Security Wizard Used to check security preferences master U/P

12 SPECIFY 6 TRAINING AGENDA Session 10: Additional/Advanced topics Georeferencing and visualizing data with Plugins Google Earth GEOLocate Producing reports and labels SpecifyiReports Construct query Link to SpecifyiReports Adding fields Specify services Manipulating the Schema config Captions Tables o Caption o Hiding tables o Usage notes o Table display format o Table aggregation o Web links Fields o Caption o Hiding field o Usage notes o Is Required o Field formatting Localization different languages WB schema config Containers and Relationships Relate collection objects in same and different collections Customizing forms

13 XML files User, User type, Collection, Discipline, Institution [discipline].views.xml (config/[discipline] directory), common.views.xml (config/common directory), global.views.xml (config/backstop directory) Eclipse (or other XML editor) Columns File structure views and viewdefs Finding correct table Specify reload forms Specify debug forms Publishing Specify data with GBIF IPT SGR Lifemapper IPT installation o Apache Tomcat o Memory allocation o IPT WAR file o Geoserver installation and configuration Specify configuration o Darwin Core schema selection o Mapping of fields o Schema export application of tab delimited data IPT and Specify integration o Source file import and upload o Viewing of data o Publishing data Specify web search client Schema mapper Data export Apache and Solr setup Download Specify web portal files Edit Solr files Customizations Future directions Specify 7 Thin client

14 Training on Data cleaning, Data quality and Data publishing through the GBIF using the IPT. Nairobi, September 2015 Organizing committee : melecoq@gbif.fr, pamerlon@gbif.fr, hbartjr@tulane.edu Training schedule Day 1 09:00 General Introduction: Short GBIF France presentation + training agenda INTRODUCTION AND DATA QUALITY 09:20 Introduction about Data Quality and Fitness for Use 10:50 Coffee Break 11:00 Methods and tools to increase the quality of biodiversity data 12:30 Lunch Break 13:30 Data standard summary and introduction to the Darwin Core Archive 15:00 Coffee Break GBIF : DATA PUBLISHING AND DATA USE 15:30 How to publish occurrence data and datasets to the GBIF (part 1) 17:00 End of session Day 2 09:00 How to publish occurrence data and datasets to the GBIF (part 2) 10:30 Coffee Break 10:45 How to discover and extract data through GBIF.org 11:45 Introduction to the Data Paper 12:45 End of training

15 Presenters: Nelson Rios and Hank Bart (2 days) Day 1 9:00-9:15 Participant Introductions 9:15-10:15 Introduction to georeferencing What is georeferencing Basic geographic concepts Polymorphic representations Paper maps Extracting coordinates Coordinate conversions Helpful online resources, Google Earth etc. 10:15-10:30 Break 10:30-11:30 GEOLocate overview 11:30-12:00 Validation 12:00-1:00 Lunch 1:00-2:00 Using GEOLocate Web Client(s) 2:00-2:45 Georeferencing exercises 2:45-3:00 Break 3:00-4:30 Georeferencing on your own Day 2 9:00-10:15 The Collaborative Georeferencing Framework Setting up user accounts Introducing the data management portal Using the Collaborative georeferencing web client 10:15-10:30 Break 9:00-10:15 The Collaborative Georeferencing Framework (continued) 10:30-12:00 Georeferencing on your own, questions etc. 12:00-1:00 Lunch 1:00-2:00 Interoperability, web services, advanced topics. 2:00-2:30 Wrap up, questions etc.

16 BHL Africa Workshop National Museum of Kenya Presenters Anne- Lise Fourie, SANBI / BHL Martin Kalfatovic, Smithsonian Libraries / BHL Carolyn Sheffield, Smithsonian Libraries / BHL Grace Costantino, Smithsonian Libraries / BHL Julia Blase, Smithsonian Libraries / BHL Agenda Overview of BHL o Structure of BHL and BHL Global o BHL Africa, Affiliate status, and relation to consortium structure o Communication channels and strategies o Discussion of 4-5 year goals for BHL Africa consortium participants BHL website o Overview, contributors and users perspectives o Titles and Items, Value- added services o How related to Internet Archive Collection Development o Scope: What do we mean by biodiversity o Deduplication, checking BHL before uploading o Copyrights and Permissions Digitization Workflow o Standards of Digitization o Gemini workflow o Metadata - including what needs to be in document so it is recognized as a BHL Africa collection o Macaw Social Media and Marketing o Strategies to promote o How we can collaborate Wrap- up o Revisit 5 year goals any changes based on information covered in training?

17 iplant Collaborative - Cyberinfrastructure for life sciences Presenter: Ramona Walls, The iplant Collaborative Do you need to share your data, images, and analyses with collaborators at multiple institutions? Do you work with big data? Have you developed a new algorithm that you want to make available to anyone to use, regardless of whether or not they have command line experience? The iplant Collaborative ( provides free cyberinfrastructure to all biologists and bioinformaticians to address these very challenges. iplant is an NSF-funded initiative with a mission to facilitate the transformation of life sciences research and education through computational infrastructure and expertise. Despite the name, iplant s scope includes any life sciences research, be it genomic or ecological, in plants, animals, or microbes, from singleresearcher investigations to community-wide collaborations. This introductory presentation will provide an overview of the tools and services available through iplant, with an emphasis on their utility to biodiversity researchers. These include: data storage, sharing, and metadata mark-up; cloud-based computing through Atmosphere; webbased access to dozens of applications through the Discovery Environment; data publishing through the iplant Data Commons; Application Programming Interfaces (APIs); image management and analysis with Bisque; and Educational, Outreach, and Training (EOT) resources. A hands-on workshop will be help during the regularly scheduled TDWG meeting, for those who want to learn more. For the complete workshop agenda, please see